Starting phenix.real_space_refine on Thu Dec 7 16:12:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/12_2023/6l4s_0833.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1410 2.51 5 N 408 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Time building chain proxies: 1.50, per 1000 atoms: 0.66 Number of scatterers: 2268 At special positions: 0 Unit cell: (83.79, 91.77, 35.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 450 8.00 N 408 7.00 C 1410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 422.8 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.361A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.585A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.275A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 93 removed outlier: 6.831A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.552A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.327A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.438A pdb=" N VAL B 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.474A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.880A pdb=" N THR D 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 92 " --> pdb=" O GLY F 93 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 54 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 402 1.28 - 1.35: 360 1.35 - 1.42: 60 1.42 - 1.49: 538 1.49 - 1.56: 914 Bond restraints: 2274 Sorted by residual: bond pdb=" CB VAL E 74 " pdb=" CG1 VAL E 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL D 74 " pdb=" CG1 VAL D 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL A 74 " pdb=" CG1 VAL A 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.46e+00 bond pdb=" CB VAL F 74 " pdb=" CG1 VAL F 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 bond pdb=" CB VAL C 74 " pdb=" CG1 VAL C 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 103.77 - 109.29: 370 109.29 - 114.81: 1120 114.81 - 120.32: 744 120.32 - 125.84: 826 125.84 - 131.35: 6 Bond angle restraints: 3066 Sorted by residual: angle pdb=" C VAL C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta sigma weight residual 121.41 113.06 8.35 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta sigma weight residual 121.41 113.08 8.33 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL D 66 " pdb=" N GLY D 67 " pdb=" CA GLY D 67 " ideal model delta sigma weight residual 121.41 113.10 8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" C VAL A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta sigma weight residual 121.41 113.11 8.30 1.96e+00 2.60e-01 1.79e+01 angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 121.41 113.12 8.29 1.96e+00 2.60e-01 1.79e+01 ... (remaining 3061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.36: 1020 7.36 - 14.71: 222 14.71 - 22.07: 78 22.07 - 29.42: 12 29.42 - 36.78: 12 Dihedral angle restraints: 1344 sinusoidal: 456 harmonic: 888 Sorted by residual: dihedral pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 289 0.087 - 0.175: 101 0.175 - 0.262: 6 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL D 95 " pdb=" CA VAL D 95 " pdb=" CG1 VAL D 95 " pdb=" CG2 VAL D 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 399 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 52 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C VAL C 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL C 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL B 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 52 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C VAL A 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 961 2.91 - 3.40: 1874 3.40 - 3.90: 3350 3.90 - 4.40: 3778 4.40 - 4.90: 7475 Nonbonded interactions: 17438 Sorted by model distance: nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR E 64 " model vdw 2.408 2.440 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR F 64 " model vdw 2.459 2.440 nonbonded pdb=" OG1 THR B 64 " pdb=" OG1 THR D 54 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP A 98 " pdb=" N GLN A 99 " model vdw 2.524 2.520 nonbonded pdb=" OD1 ASP F 98 " pdb=" N GLN F 99 " model vdw 2.524 2.520 ... (remaining 17433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.940 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.070 2274 Z= 0.956 Angle : 1.363 8.347 3066 Z= 0.791 Chirality : 0.091 0.436 402 Planarity : 0.006 0.023 384 Dihedral : 10.279 36.779 780 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.35), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.015 0.007 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2235 time to fit residues: 18.9606 Evaluate side-chains 75 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2274 Z= 0.233 Angle : 0.621 4.481 3066 Z= 0.340 Chirality : 0.052 0.158 402 Planarity : 0.002 0.015 384 Dihedral : 6.210 17.232 324 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.39 % Allowed : 21.93 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.010 0.002 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.329 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.2188 time to fit residues: 19.4047 Evaluate side-chains 76 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0270 time to fit residues: 0.7827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2274 Z= 0.143 Angle : 0.518 4.060 3066 Z= 0.285 Chirality : 0.050 0.145 402 Planarity : 0.002 0.011 384 Dihedral : 5.257 14.688 324 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.75 % Allowed : 23.68 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.245 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.2226 time to fit residues: 17.5233 Evaluate side-chains 65 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.231 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0252 time to fit residues: 0.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2274 Z= 0.157 Angle : 0.497 4.356 3066 Z= 0.272 Chirality : 0.051 0.141 402 Planarity : 0.002 0.008 384 Dihedral : 5.082 14.283 324 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.63 % Allowed : 22.81 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F 50 PHE 0.006 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.251 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.2112 time to fit residues: 17.8350 Evaluate side-chains 72 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0248 time to fit residues: 0.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 overall best weight: 4.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2274 Z= 0.322 Angle : 0.597 5.418 3066 Z= 0.327 Chirality : 0.052 0.154 402 Planarity : 0.002 0.009 384 Dihedral : 5.780 15.343 324 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.07 % Allowed : 25.00 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.268 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2195 time to fit residues: 18.2452 Evaluate side-chains 75 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0812 time to fit residues: 0.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN F 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2274 Z= 0.151 Angle : 0.506 4.118 3066 Z= 0.275 Chirality : 0.051 0.148 402 Planarity : 0.002 0.010 384 Dihedral : 5.107 14.308 324 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.19 % Allowed : 24.56 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.342 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.2191 time to fit residues: 17.2360 Evaluate side-chains 65 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0283 time to fit residues: 0.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.0170 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 19 optimal weight: 0.0050 chunk 14 optimal weight: 7.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2274 Z= 0.119 Angle : 0.487 4.287 3066 Z= 0.262 Chirality : 0.051 0.140 402 Planarity : 0.002 0.012 384 Dihedral : 4.607 14.183 324 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.32 % Allowed : 25.00 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.252 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 67 average time/residue: 0.2370 time to fit residues: 17.4522 Evaluate side-chains 63 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.229 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0246 time to fit residues: 0.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.0000 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2274 Z= 0.230 Angle : 0.566 5.898 3066 Z= 0.306 Chirality : 0.051 0.148 402 Planarity : 0.002 0.013 384 Dihedral : 5.141 14.525 324 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.32 % Allowed : 24.56 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.005 0.001 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.258 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.2150 time to fit residues: 17.1228 Evaluate side-chains 70 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0236 time to fit residues: 0.4053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 0.0770 overall best weight: 3.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2274 Z= 0.262 Angle : 0.585 5.202 3066 Z= 0.315 Chirality : 0.051 0.152 402 Planarity : 0.002 0.018 384 Dihedral : 5.397 14.473 324 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.44 % Allowed : 26.32 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.003 0.001 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.245 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.2156 time to fit residues: 17.5373 Evaluate side-chains 72 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2274 Z= 0.328 Angle : 0.672 6.736 3066 Z= 0.361 Chirality : 0.052 0.158 402 Planarity : 0.002 0.018 384 Dihedral : 5.734 15.664 324 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.44 % Allowed : 28.07 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE A 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.243 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.2166 time to fit residues: 17.1115 Evaluate side-chains 69 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0238 time to fit residues: 0.3453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.171620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.131229 restraints weight = 2553.921| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 3.65 r_work: 0.4029 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2274 Z= 0.354 Angle : 0.708 6.614 3066 Z= 0.380 Chirality : 0.053 0.160 402 Planarity : 0.003 0.021 384 Dihedral : 5.883 16.111 324 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.88 % Allowed : 26.75 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1004.50 seconds wall clock time: 18 minutes 57.33 seconds (1137.33 seconds total)